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Question: RPKM to FPKM conversion
0
gravatar for kanwarjag
3.6 years ago by
kanwarjag • 990
United States
kanwarjag • 990 wrote:

I have RNAseq data as RPKM values (tumor vs normal)  since data is paired end how could I convert to FPKM values. 

Thanks

 
rna-seq • 3.6k views
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modified 3.6 years ago by michael.ante • 3.4k • written 3.6 years ago by kanwarjag • 990
1

You may/should not convert RPKM to FPKM. You need to recalculate FPKM from BAM file. As suggested below, if you just divide by 2, they wont be true FPKM values as you do not knowif there are any read-pairs with only one-end mapped. And if there are many read pairs like that your FPKM value might not be true.

ADD REPLY • link modified 12 months ago by RamRS ♦ 24k • written 3.6 years ago by geek_y ♦ 9.8k

Thanks for the explanation

ADD REPLY • link modified 12 months ago by RamRS ♦ 24k • written 3.6 years ago by kanwarjag • 990
2
gravatar for michael.ante
3.6 years ago by
michael.ante • 3.4k
Austria/Vienna
michael.ante • 3.4k wrote:

In case of single end data, RPKM=FPKM (Reads per kilobase per million reads and Fragments per kilobase per million reads).

In case of paired end data, you have for every read-pair one fragment. Thus, divide the RPKM by two.
ADD COMMENT • link modified 12 months ago by RamRS ♦ 24k • written 3.6 years ago by michael.ante • 3.4k

very naive clarification should it be tumor RPKM/2 - normal RPKM/2

or it should be tumor RPKM-normal RPKM = X/2

ADD REPLY • link modified 12 months ago by RamRS ♦ 24k • written 3.6 years ago by kanwarjag • 990

If you are looking at the ratios/fold-changes, it doesn't matter. The factor 2 is cancelled:

4:1 == 2:0.5
ADD REPLY • link modified 12 months ago by RamRS ♦ 24k • written 3.6 years ago by michael.ante • 3.4k

got it 

ADD REPLY • link modified 3.6 years ago • written 3.6 years ago by kanwarjag • 990
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